diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 54ca187658cc5c11771028847fd635b820792d2a..b428b0bc77f391c9d276e5bd604763b3e1d41b7b 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -229,14 +229,14 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
         design_new_df.at[3, 'tag_align'] = design_new_df.at[0, 'tag_align']
 
         # Make 2 self psuedoreplicates
-        pool_pseudoreplicates_dict = {}
+        self_pseudoreplicates_dict = {}
         for rep, tag_file in zip(design_df['replicate'], design_df['tag_align']):
             replicate_prefix = experiment_id + '_' + str(rep)
-            pool_pseudoreplicates_dict = \
+            self_pseudoreplicates_dict = \
                 self_psuedoreplication(tag_file, replicate_prefix, paired)
 
         # Update design to include new self pseudo replicates
-        for rep, pseudorep_file in pool_pseudoreplicates_dict.items():
+        for rep, pseudorep_file in self_pseudoreplicates_dict.items():
             path_to_file = cwd + '/' + pseudorep_file
             replicate = rep + 1
             design_new_df.loc[replicate, 'tag_align'] = path_to_file
@@ -312,25 +312,25 @@ def generate_design(paired, cutoff_ratio, design_df, cwd, no_reps, no_unique_con
         path_to_pool_control = cwd + '/' +  pool_control
         design_new_df['control_tag_align'] = path_to_pool_control
 
-    # Add in pseudo replicates
-    tmp_metadata = design_new_df.loc[0].copy()
-    tmp_metadata['control_tag_align'] = path_to_pool_control
-    for rep, pseudorep_file in pool_pseudoreplicates_dict.items():
-        tmp_metadata['sample_id'] = experiment_id + '_pr' + str(rep)
-        tmp_metadata['replicate'] = str(rep) + '_pr'
+        # Add in pseudo replicates
+        tmp_metadata = design_new_df.loc[0].copy()
+        tmp_metadata['control_tag_align'] = path_to_pool_control
+        for rep, pseudorep_file in pool_pseudoreplicates_dict.items():
+            tmp_metadata['sample_id'] = experiment_id + '_pr' + str(rep)
+            tmp_metadata['replicate'] = str(rep) + '_pr'
+            tmp_metadata['xcor'] = 'Calculate'
+            path_to_file = cwd + '/' + pseudorep_file
+            tmp_metadata['tag_align'] = path_to_file
+            design_new_df = design_new_df.append(tmp_metadata)
+
+        # Add in pool experiment
+        tmp_metadata['sample_id'] = experiment_id + '_pooled'
+        tmp_metadata['replicate'] = 'pooled'
         tmp_metadata['xcor'] = 'Calculate'
-        path_to_file = cwd + '/' + pseudorep_file
+        path_to_file = cwd + '/' + pool_experiment_se
         tmp_metadata['tag_align'] = path_to_file
         design_new_df = design_new_df.append(tmp_metadata)
 
-    # Add in pool experiment
-    tmp_metadata['sample_id'] = experiment_id + '_pooled'
-    tmp_metadata['replicate'] = 'pooled'
-    tmp_metadata['xcor'] = 'Calculate'
-    path_to_file = cwd + '/' + pool_experiment_se
-    tmp_metadata['tag_align'] = path_to_file
-    design_new_df = design_new_df.append(tmp_metadata)
-
     return design_new_df